diff imagej2_noise_jython_script.py @ 0:018144807556 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_noise_jython_script.py	Tue Sep 24 17:12:52 2024 +0000
@@ -0,0 +1,56 @@
+import sys
+
+from ij import IJ, ImagePlus
+
+# Fiji Jython interpreter implements Python 2.5 which does not
+# provide support for argparse.
+input_file = sys.argv[-8]
+image_datatype = sys.argv[-7]
+noise = sys.argv[-6]
+standard_deviation = sys.argv[-5]
+radius = sys.argv[-4]
+threshold = sys.argv[-3]
+which_outliers = sys.argv[-2]
+tmp_output_path = sys.argv[-1]
+
+# Open the input image file.
+image_plus = IJ.openImage(input_file)
+image_type = image_plus.getType()
+is32BITS_GREY = image_type == ImagePlus.GRAY32
+# Create an ImagePlus object for the image.
+image_plus_copy = image_plus.duplicate()
+
+# Perform the analysis on the ImagePlus object.
+try:
+    if noise == "add_noise":
+        IJ.run(image_plus_copy, "Add Noise", "")
+    elif noise == "add_specified_noise":
+        IJ.run(image_plus_copy, "Add Specified Noise...", "standard=%s" % standard_deviation)
+    elif noise == "salt_and_pepper":
+        IJ.run(image_plus_copy, "Salt and Pepper", "")
+    elif noise == "despeckle":
+        IJ.run(image_plus_copy, "Despeckle", "")
+    elif noise == "remove_outliers":
+        IJ.run(
+            image_plus_copy,
+            "Remove Outliers...",
+            "radius=%s threshold=%s which=%s" % (radius, threshold, which_outliers)
+        )
+    elif noise == "remove_nans":
+        if is32BITS_GREY:
+            IJ.run(image_plus_copy, "Remove NaNs...", "")
+        else:
+            raise Exception("Remove NaNs can only be applied to 32bits grey images.")
+    elif noise == "rof_denoise":
+        if is32BITS_GREY:
+            IJ.run(image_plus_copy, "ROF Denoise", "")
+        else:
+            raise Exception("ROF Denoise can only be applied to 32bits grey images.")
+except Exception as e:
+    # This is due to some operations like remove_outliers and despeckle which block the script
+    print(e)
+    exit(1)
+# Save the ImagePlus object as a new image.
+IJ.saveAs(image_plus_copy, image_datatype, tmp_output_path)
+# This is due to some operations like remove_outliers and despeckle which block the script
+exit(0)